Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing.

As the availability of data sets increases, meta-analysis leveraging aggregated and interoperable data types is proving valuable. This study leveraged a meta-analysis workflow to identify mutations that could improve robustness to reactive oxygen species (ROS) stresses using an industrially important melatonin production strain as an example. ROS stresses often occur during cultivation and negatively affect strain performance. Cellular response to ROS is also linked to the SOS response and resistance to pH fluctuations, which is important to strain robustness in large-scale biomanufacturing. This work integrated more than 7000 E. coli adaptive laboratory evolution (ALE) mutations across 59 experiments to statistically associate mutated genes to 2 ROS tolerance ALE conditions from 72 unique conditions. Mutant oxyR, fur, iscR, and ygfZ were significantly associated and hypothesized to contribute fitness in ROS stress. Across these genes, 259 total mutations were inspected in conjunction with transcriptomics from 46 iModulon experiments. Ten mutations were chosen for reintroduction based on mutation clustering and coinciding transcriptional changes as evidence of fitness impact. Strains with mutations reintroduced into oxyR, fur, iscR, and ygfZ exhibited increased tolerance to H2O2 and acid stress and reduced SOS response, all of which are related to ROS. Additionally, new evidence was generated toward understanding the function of ygfZ, an uncharacterized gene. This meta-analysis approach utilized aggregated and interoperable multiomics data sets to identify mutations conferring industrially relevant phenotypes with the least drawbacks, describing an approach for data-driven strain engineering to optimize microbial cell factories.

Biarticular muscles in light of template models, experiments and robotics: a review.

Leg morphology is an important outcome of evolution. A remarkable morphological leg feature is the existence of biarticular muscles that span adjacent joints. Diverse studies from different fields of research suggest a less coherent understanding of the muscles' functionality in cyclic, sagittal plane locomotion. We structured this review of biarticular muscle function by reflecting biomechanical template models, human experiments and robotic system designs. Within these approaches, we surveyed the contribution of biarticular muscles to the locomotor subfunctions (stance, balance and swing). While mono- and biarticular muscles do not show physiological differences, the reviewed studies provide evidence for complementary and locomotor subfunction-specific contributions of mono- and biarticular muscles. In stance, biarticular muscles coordinate joint movements, improve economy (e.g. by transferring energy) and secure the zig-zag configuration of the leg against joint overextension. These commonly known functions are extended by an explicit role of biarticular muscles in controlling the angular momentum for balance and swing. Human-like leg arrangement and intrinsic (compliant) properties of biarticular structures improve the controllability and energy efficiency of legged robots and assistive devices. Future interdisciplinary research on biarticular muscles should address their role for sensing and control as well as non-cyclic and/or non-sagittal motions, and non-static moment arms.

Stereoselective Aromatic Ring Hydrogenation over Supported Rhodium Catalysts in Supercritical Carbon Dioxide Solvent.

The combination of supported rhodium metal catalysts and supercritical carbon dioxide solvent was effective for the stereoselective ring hydrogenations of aromatic compounds at low temperature. Higher solubility of hydrogen in supercritical carbon dioxide provides higher concentration of hydrogen on the rhodium surface, but lower that of the intermediate on rhodium surface, which suppresses the flipping of surface intermediate, leading to higher catalyst activities and cis selectivities to the corresponding ring-hydrogenated products as compared with those in organic solvents.

Influence of striking technique on maximum striking velocities-experimental and statistical investigation.

Forensic experts often have to assess injury and fatality risks in the context of violent blunt force trauma. Maximum striking velocities in one- and two-handed strikes with a rod-like implement can be of particular interest. Current literature lacks studies addressing this problem. The purpose of this study was therefore to measure and analyse maximum striking velocities in one-handed and two-handed strikes in female and male volunteers. We hypothesised higher striking velocities in two-handed strikes compared to one-handed strikes. Fifty volunteers performed one- and two-handed strikes from top to bottom using a steel rod of 65 cm length and 1000 g weight. A Qualisys™ Motion Analysis system registered displacements of reflecting markers fixed to the rod as well as to the volunteer's body. In one-handed strikes, the mean maximum striking velocity was 17.2 m/s in the female sample and 23.9 m/s in the male sample. Statistically not significantly different maximum striking velocities were found in two-handed strikes with mean values of 18.3 m/s in the female sample and 24.2 m/s in the male sample. Female and male volunteers also yielded similar mean maximum striking velocities in two-handed strikes comparing 'overhead' and 'overshoulder' striking techniques. In conclusion, the striking technique did not relevantly influence maximum striking velocities in our setup.

Maximum striking velocities in strikes with steel rods-the influence of rod length, rod mass and volunteer parameters.

In blunt force trauma to the head caused by attacks with blunt instruments, contact forces can be estimated based on the conservation of momentum if impact velocities are known. The aims of this work were to measure maximum striking velocities and to examine the influence of rod parameters such as rod mass and length as well as volunteer parameters such as sex, age, body height, body mass, body mass index and the average amount of physical exercise. Steel rods with masses of 500, 1000 and 1500 g as well as lengths of 40, 65 and 90 cm were exemplarily tested as blunt instruments. Twenty-nine men and 22 women participated in this study. Each volunteer performed several vertical strikes with the steel rods onto a passive immobile target. Maximum striking velocities were measured by means of a Qualisys motion capture system using high-speed cameras and infrared light. Male volunteers achieved maximum striking velocities between 14.0 and 35.5 m/s whereas female volunteers achieved values between 10.4 and 28.3 m/s. Results show that maximum striking velocities increased with smaller rod masses and less consistently with higher rod lengths. Statistically significant influences were found in the volunteers' sex and average amount of physical exercise.

Diagnosing peri-implant disease using the tongue as a 24/7 detector.

Our ability of screening broad communities for clinically asymptomatic diseases critically drives population health. Sensory chewing gums are presented targeting the tongue as 24/7 detector allowing diagnosis by "anyone, anywhere, anytime". The chewing gum contains peptide sensors consisting of a protease cleavable linker in between a bitter substance and a microparticle. Matrix metalloproteinases in the oral cavity, as upregulated in peri-implant disease, specifically target the protease cleavable linker while chewing the gum, thereby generating bitterness for detection by the tongue. The peptide sensors prove significant success in discriminating saliva collected from patients with peri-implant disease versus clinically asymptomatic volunteers. Superior outcome is demonstrated over commercially available protease-based tests in saliva. "Anyone, anywhere, anytime" diagnostics are within reach for oral inflammation. Expanding this platform technology to other diseases in the future features this diagnostic as a massive screening tool potentially maximizing impact on population health.Early detection of gum inflammation caused by dental implants helps prevent tissue damage. Here, the authors present a peptide sensor that generates a bitter taste when cleaved by proteases present in peri-implant disease, embed it in a chewing gum, and compare the probe to existing sensors using patient saliva.

A method to minimize the global warming and environmental pollution.

There has been continuous increase in the level of CO2 in atmosphere. Therefore, it is essential to develop an economical and convenient process to reduce the concentration of CO2 in the atmosphere. In this study, we have proposed an economical and efficient adsorption method to minimize the environmental CO2. A fluidized bed adsorption column was used, fabricated using cast iron sheet. The low prize pyrolyzed biochar prepared from farming biomass (crushed fine powder) was used as an adsorbent to adsorb CO2 from the mixture of air and CO2 (99.5% air and 0.5% CO2). The experimental observation was taken for the % removal of CO2 from the mixture of air and CO2, development of adsorption isotherm and to study the effect of pressure and inlet gas flow rate on the amount of CO2 adsorbed per kg of biochar. The exhausted (CO2 adsorbed) biochar from the fluidized column was tested as a fertilizer for the wheat crop and it has given near about 10% increase in the height of wheat crop within the first 10 days after sowing the wheat seeds. On the basis of this experimentation, we have proposed a hypothetical method, using above mentioned fluidized bed column and biochar as adsorbent to reduce the CO2 concentration in the highly polluted regions.

Effect of calcination cycles on the preparation of tin oxide based traditional drug: studies on its formation and characterization.

The preparation method of metal based Indian traditional drugs involves conversion of a pure metal into its oxide by repeated high temperature calcination cycles. In this work, the effect of number of calcination cycles followed in the preparation of tin oxide based Ayurvedic drug, 'vanga bhasma' was studied by a systematic characterization of the drug samples after various calcination stages. It was found that tin was in the form of Sn4+ state and that the formation of SnO2 proceeded step-wise through Sn(OH)4.

Detection limit of methods to assess fluid status changes in dialysis patients.

Technical systems for an accurate and practicable fluid management of dialysis patients are urgently needed, since current clinical methods are partially subjective, imprecise, and time consuming. Such new systems should not only allow the determination of the target normohydration weight, but also must be able to detect clinically relevant changes in fluid volume ( approximately 1 l). This study focuses on the systematic analysis of the detection limit of several candidate methods for fluid management. In a cohort of 16 new dialysis patients, several candidate methods were applied in parallel during each treatment of the initial weight reduction phase: the measurement of vena cava diameter (VCD), vena cava collapsibility index (CI), the blood volume drop during an ultrafiltration (UF) bolus (Deltarelative blood volume (RBV)-), the rebound after the UF bolus (DeltaRBV+), and the extracellular fluid volume determined with whole body bioimpedance spectroscopy (BIS). A clinical reference method was used to manage the fluid status of patients. All methods showed significant correlations with predialysis weight. The detection limits W(lim) of candidate methods for changes in fluid status were assessed as W(lim)=0.87 kg+/-0.64 kg (BIS), 1.74 kg+/-1.56 kg (VCD), 2.3 kg+/-1.0 kg (DeltaRBV-), 7.4 kg+/-8.5 kg (CI), 40 kg+/-108 kg (DeltaRBV+). Only BIS shows a satisfactorily low detection limit W(lim), whereas W(lim) was rated as critical for the VCD and DeltaRBV- methods, and as unacceptable for the CI and DeltaRBV+ methods. Bioimpedance spectroscopy appears to be the most promising method for a practical fluid management system in dialysis.

Preparation and characterization of a copper based Indian traditional drug: tamra bhasma.

The copper based Indian traditional drug 'tamra bhasma' is administered for various ailments since long. Its synthesis involves treating metallic copper with plant juices and then repeated calcination in presence of air so that the metallic state is transformed into the corresponding oxide form traditionally known as 'bhasma'. In this work, we present a systematic characterization of this traditional drug using various techniques like X-ray diffraction (XRD), scanning electron microscopy (SEM)-energy dispersive X-ray analysis (EDX), X-ray photoelectron spectroscopy (XPS), infrared spectroscopy (IR), thermogravimetry (TG) and surface area measurement. The results obtained were found to match very well with those of a standard copper oxide confirming the composition of the drug sample. In addition, some specific findings were also made which could help in interpreting the therapeutic properties of the traditional drug 'tamra bhasma'.

Extracorporeal pressure monitoring and the detection of vascular access stenosis.

Prospective monitoring of static venous pressure is an established tool to detect outflow stenoses in a vascular access. However, with this method it is not possible to identify vascular stenoses which are localized between the arterial and venous dialysis needle. We describe a new approach based on both static arterial and venous extracorporeal pressures. Pressure data of 9 dialysis patients with normal vascular access function and 9 patients with stenotic access were analyzed. Extracorporeal pressure was found to depend on the position of the heart relative to the extracorporeal blood circuit. All patients with venous outflow stenoses had an elevated ratio of arterial and venous intra-access pressure to mean arterial pressure. In case of access stenosis between arterial and venous needle the ratio of venous pressure to mean arterial pressure was normal, and only the arterial pressure ratio was elevated. We conclude that combined arterial and venous intraaccess pressure measurement normalized by mean blood pressure detects venous stenosis as well as stenosis between the arterial and venous dialysis needle. To minimize the rate of access thrombosis both arterial and venous intra-access pressure should be monitored.

Integrated genomic map from uropathogenic Escherichia coli J96.

Escherichia coli J96 is a uropathogen having both broad similarities to and striking differences from nonpathogenic, laboratory E. coli K-12. Strain J96 contains three large (>100-kb) unique genomic segments integrated on the chromosome; two are recognized as pathogenicity islands containing urovirulence genes. Additionally, the strain possesses a fourth smaller accessory segment of 28 kb and two deletions relative to strain K-12. We report an integrated physical and genetic map of the 5,120-kb J96 genome. The chromosome contains 26 NotI, 13 BlnI, and 7 I-CeuI macrorestriction sites. Macrorestriction mapping was rapidly accomplished by a novel transposon-based procedure: analysis of modified minitransposon insertions served to align the overlapping macrorestriction fragments generated by three different enzymes (each sharing a common cleavage site within the insert), thus integrating the three different digestion patterns and ordering the fragments. The resulting map, generated from a total of 54 mini-Tn10 insertions, was supplemented with auxanography and Southern analysis to indicate the positions of insertionally disrupted aminosynthetic genes and cloned virulence genes, respectively. Thus, it contains not only physical, macrorestriction landmarks but also the loci for eight housekeeping genes shared with strain K-12 and eight acknowledged urovirulence genes; the latter confirmed clustering of virulence genes at the large unique accessory chromosomal segments. The 115-kb J96 plasmid was resolved by pulsed-field gel electrophoresis in NotI digests. However, because the plasmid lacks restriction sites for the enzymes BlnI and I-CeuI, it was visualized in BlnI and I-CeuI digests only of derivatives carrying plasmid inserts artificially introducing these sites. Owing to an I-SceI site on the transposon, the plasmid could also be visualized and sized from plasmid insertion mutants after digestion with this enzyme. The insertional strains generated in construction of the integrated genomic map provide useful physical and genetic markers for further characterization of the J96 genome.

When and why do people avoid unknown probabilities in decisions under uncertainty? Testing some predictions from optimal foraging theory.

When given a choice between two otherwise equivalent options - one in which the probability information is stated and another in which it is missing - most people avoid the option with missing probability information (Camerer & Weber, 1992). This robust, frequently replicated tendency is known as the ambiguity effect. It is unclear, however, why the ambiguity effect occurs. Experiments 1 and 2, which separated effects of the comparison process from those related to missing probability information, demonstrate that the ambiguity effect is elicited by missing probabilities rather than by comparison of options. Experiments 3 and 4 test predictions drawn from the literature on behavioral ecology. It is suggested that choices between two options should reflect three parameters: (1) the need of the organism, (2) the mean expected outcome of each option; and (3) the variance associated with each option's outcome. It is hypothesized that unknown probabilities are avoided because they co-occur with high outcome variability. In Experiment 3 it was found that subjects systematically avoid options with high outcome variability regardless of whether probabilities are explicitly stated or not. In Experiment 4, we reversed the ambiguity effect: when participants' need was greater than the known option's expected mean outcome, subjects preferred the ambiguous (high variance) option. From these experiments we conclude that people do not generally avoid ambiguous options. Instead, they take into account expected outcome, outcome variability, and their need in order to arrive at a decision that is most likely to satisfy this need.

The Pediatric Cancer Quality of Life Inventory-32 (PCQL-32). II. Feasibility and range of measurement.

The Pediatric Cancer Quality of Life Inventory-32 (PCQL-32) has been developed to be a standardized assessment instrument to assess systematically pediatric cancer patient's health-related quality of life (HRQOL) outcomes. Multidimensional serial measurement of pediatric cancer patients' HRQOL in Phase III randomized controlled clinical trials is increasingly being recognized as an essential component in evaluating the comprehensive health outcomes of modern antineoplastic treatment protocols. The 32-item PCQL-32 short form was empirically derived from the PCQL long form (84-87 items), which was administered to 291 pediatric cancer patients and their parents during various stages of treatment. The feasibility (percentage of missing values per item) and range of measurement [percentage of minimum (floor effect) and maximum (ceiling effect) possible scores] was calculated for the five PCQL-32 scales and the total scale score. Feasibility for the PCQL-32 was very good, with less than .01% missing values. Range of measurement was full, with no ceiling effects (higher symptoms/problems) and low to moderate floor effects (lower symptoms/problems). The PCQL-32 demonstrated very good feasibility and range of measurement. In its short form, the PCQL-32 is practical for Phase III clinical trials. Future studies will test the utility of the PCQL-32 as a brief serial measure for monitoring the HRQOL outcomes for children and adolescents with cancer.

The PedsQL: measurement model for the pediatric quality of life inventory.

BACKGROUND: Pediatric patients' self-report of health-related quality of life (HRQOL) has emerged as an important patient-based health outcome. A practical, validated generic measure of HRQOL facilitates assessing risk, tracking health status, and measuring treatment outcomes in pediatric populations. METHODS: The PedsQL is a brief, standardized, generic assessment instrument that systematically assesses patients' and parents' perceptions of HRQOL in pediatric patients with chronic health conditions using pediatric cancer as an exemplary model. The PedsQL is based on a modular approach to measuring HRQOL and consists of a 15-item core measure of global HRQOL and eight supplemental modules assessing specific symptom or treatment domains. The PedsQL was empirically derived from data collected from 291 pediatric cancer patients and their parents at various stages of treatment. RESULTS: Both reliability and validity were determined. Cronbach's alpha coefficients for the core measure (alpha = .83 for patient and alpha = .86 for parent) were acceptable for group comparisons. Alphas for the patient self-report modules generally ranged from .70 to .89. Discriminant or clinical validity, using the known-groups approach, was demonstrated for patients on- versus off-treatments. The 11 scales showed small-to-medium positive intercorrelations, supporting the multidimensional measurement model. Further construct validity was demonstrated via a multimethod-multitrait matrix using standardized psychosocial questionnaires. CONCLUSION: The results support the PedsQL as a reliable and valid measure of HRQOL. The PedsQL core and modular design makes it flexible enough to be used in a variety of research and clinical applications for pediatric chronic health conditions.

Type-specific contributions to chromosome size differences in Escherichia coli.

The Escherichia coli genome varies in size from 4.5 to 5.5 Mb. It is unclear whether this variation may be distributed finely throughout the genome or is concentrated at just a few chromosomal loci or on plasmids. Further, the functional correlates of size variation in different genome copies are largely unexplored. We carried out comparative macrorestriction mapping using rare-restriction-site alleles (made with the Tn10dRCP2 family of elements, containing the NotI, BlnI, I-CeuI, and ultra-rare-cutting I-SceI sites) among the chromosomes of laboratory E. coli K-12, newborn-sepsis-associated E. coli RS218, and uropathogenic E. coli J96. These comparisons showed just a few large accessory chromosomal segments accounting for nearly all strain-to-strain size differences. Of 10 sepsis-associated and urovirulence genes, previously isolated from the two pathogens by scoring for function, all were colocalized exclusively with one or more of the accessory chromosomal segments. The accessory chromosomal segments detected in the pathogenic strains from physical, macrorestriction comparisons may be a source of new virulence genes, not yet isolated by function.

The Pediatric Cancer Quality of Life Inventory: a modular approach to measuring health-related quality of life in children with cancer.

Measurement of pediatric cancer patients' health-related quality of life (HRQL) in phase III randomized, controlled clinical trials is being recognized increasingly as an essential component in evaluating the comprehensive health outcomes of modern anti-neoplastic treatment protocols. Use of a brief core measure of HRQL plus disease-specific symptom modules is a way to assess specific HRQL outcomes with a minimum of subject burden. Demonstrating a measure's feasibility, reliability and validity also represents children's ability to provide reliable and valid responses to HRQL questions. The Pediatric Cancer Quality of Life Inventory (PCQL) Modular Approach consists of a 15-item core measure of HRQL and 2 specific symptom modules: pain and nausea. To validate a patient-report form and a parent-report form, the PCQL was administered to 291 pediatric cancer patients and to their parents. Feasibility and range of measurement, as well as patient-parent concordance, were assessed. Internal consistency reliability was assessed via Cronbach's alpha. Validity was determined by the known-groups approach and by correlating PCQL scores with days missed from school. Patients had minimal missing data, and the range of measurement for the items was good. Patient-parent concordance was large but not perfect. For both patient and parent forms, internal consistency reliability of the PCQL core scale (0.83 and 0. 86, respectively) was strong. The internal consistency reliabilities of the 2 symptom modules for both patient and parent forms were in the acceptable range for group comparisons. Regarding clinical validity, the core scale and the 2 symptom modules distinguished between patients on and off treatment for both patient and parent reports. Further, both patient and parent reports correlated with days of missed school in the past 6 and 12 months. The PCQL Modular Approach has demonstrated acceptable internal consistency reliability and clinical validity for both patient-report and parent-report forms. By implication, children are capable of providing reliable and valid responses to these HRQL questions.

Subdivision of the Escherichia coli K-12 genome for sequencing: manipulation and DNA sequence of transposable elements introducing unique restriction sites.

A transposon-based method of introducing unique restriction sites was used for subdivision of the Escherichia coli genome into a contiguous series of large non-overlapping segments spanning 2.5Mb. The segments, sizes ranging from 150 to 250kb, were isolated from the chromosome using the inserted restriction sites and shotgun cloned into an M13 vector for DNA sequencing. These shotgun sizes proved easily manageable, allowing the genomic sequence of E. coli to be completed more efficiently and rapidly than was possible by previously available methods. The 9bp duplication generated during transposition was used as a tag for accurate splicing of the segments; no further sequence redundancy at the junction sites was needed. The system is applicable to larger genomes even if they are not already well-characterized. We present the technology for segment sequencing, results of applying this method to E. coli, and the sequences of the transposon cassettes.

"Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli.

Plasmids, bacteriophages, and pathogenicity islands are genomic additions that contribute to the evolution of bacterial pathogens. For example, Shigella spp., the causative agents of bacillary dysentery, differ from the closely related commensal Escherichia coli in the presence of a plasmid in Shigella that encodes virulence functions. However, pathogenic bacteria also may lack properties that are characteristic of nonpathogens. Lysine decarboxylase (LDC) activity is present in approximately 90% of E. coli strains but is uniformly absent in Shigella strains. When the gene for LDC, cadA, was introduced into Shigella flexneri 2a, virulence became attenuated, and enterotoxin activity was inhibited greatly. The enterotoxin inhibitor was identified as cadaverine, a product of the reaction catalyzed by LDC. Comparison of the S. flexneri 2a and laboratory E. coli K-12 genomes in the region of cadA revealed a large deletion in Shigella. Representative strains of Shigella spp. and enteroinvasive E. coli displayed similar deletions of cadA. Our results suggest that, as Shigella spp. evolved from E. coli to become pathogens, they not only acquired virulence genes on a plasmid but also shed genes via deletions. The formation of these "black holes," deletions of genes that are detrimental to a pathogenic lifestyle, provides an evolutionary pathway that enables a pathogen to enhance virulence. Furthermore, the demonstration that cadaverine can inhibit enterotoxin activity may lead to more general models about toxin activity or entry into cells and suggests an avenue for antitoxin therapy. Thus, understanding the role of black holes in pathogen evolution may yield clues to new treatments of infectious diseases.

The complete genome sequence of Escherichia coli K-12.

The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.